Bug NCBI FTP

goci-core/goci-db-binding/src/main/resources/db/migration/V2.3.0_003__NCBI_Catalog_Summary_View_Hotfix.sql

@@ -0,0 +1,112 @@
+/*################################################################################
+
+Fixing bug header NCBI_CATALOG_SUMMARY_VIEW
+
+author:  C Malangone
+date:    March 2018
+version: 2.3.0.003
+################################################################################
+*/
+
+CREATE OR REPLACE  VIEW NCBI_CATALOG_SUMMARY_VIEW AS
+  SELECT
+    ROWNUM as ID,
+    V."STUDY_ADDED_DATE",
+    V."PUBMED_ID",
+    V."AUTHOR",
+    V."PUBLICATION_DATE",
+    V."JOURNAL",
+    V."LINK",
+    V."STUDY",
+    V."DISEASE_TRAIT",
+    V."INITIAL_SAMPLE_DESCRIPTION",
+    V."REPLICATE_SAMPLE_DESCRIPTION",
+    V."REGION",
+    V."REPORTED_GENE",
+    V."STRONGEST_SNP_RISK_ALLELE",
+    V."SNP_RS_ID" AS SNP_RSID,
+    V."SNP_ID",
+    V."RISK_ALLELE_FREQUENCY",
+    V."P_VALUE_MANTISSA",
+    V."P_VALUE_EXPONENT",
+    V."P_VALUE_QUALIFIER",
+    V."OR_BETA",
+    V."CI",
+    V."CI_QUALIFIER",
+    V."MANUFACTURER",
+    V."QUALIFIER",
+    V."SNP_COUNT",
+    V."IMPUTED",
+    V."STUDY_DESIGN_COMMENT",
+    V."PLATFORM",
+    V."CNV",
+    V."ASSOCIATION_ID",
+    V."STUDY_ID",
+    V."CATALOG_PUBLISH_DATE",
+    V."CATALOG_UNPUBLISH_DATE",
+    V."TRAIT" AS EFO_TRAIT,
+    V."URI" AS EFO_URI
+  FROM
+    (SELECT
+       h.STUDY_ADDED_DATE,
+       pub.PUBMED_ID,
+       auth.FULLNAME_STANDARD AS author,
+       pub.PUBLICATION_DATE,
+       pub.PUBLICATION                                             AS JOURNAL,
+       CONCAT('http://europepmc.org/abstract/MED/', pub.PUBMED_ID) AS LINK,
+       pub.TITLE                                                   AS STUDY,
+       dt.TRAIT                                                  AS DISEASE_TRAIT,
+       s.INITIAL_SAMPLE_SIZE                                     AS INITIAL_SAMPLE_DESCRIPTION,
+       s.REPLICATE_SAMPLE_SIZE                                   AS REPLICATE_SAMPLE_DESCRIPTION,
+       r.NAME                                                    AS REGION,
+       rg.GENE_NAME                                              AS REPORTED_GENE,
+       ra.RISK_ALLELE_NAME                                       AS STRONGEST_SNP_RISK_ALLELE,
+       snp.RS_ID                                                 AS SNP_RS_ID,
+       snp.ID                                                    AS SNP_ID,
+       a.RISK_FREQUENCY                                          AS RISK_ALLELE_FREQUENCY,
+       a.PVALUE_MANTISSA                                         AS P_VALUE_MANTISSA,
+       a.PVALUE_EXPONENT                                         AS P_VALUE_EXPONENT,
+       a.PVALUE_DESCRIPTION                                      AS P_VALUE_QUALIFIER,
+       (CASE WHEN a.OR_PER_COPY_NUM IS NOT NULL
+         THEN a.OR_PER_COPY_NUM
+        ELSE a.BETA_NUM END)                                     AS OR_BETA,
+       a.RANGE                                                   AS CI,
+       (CASE WHEN a.BETA_UNIT IS NOT NULL AND a.BETA_DIRECTION IS NOT NULL
+         THEN CONCAT(CONCAT(a.BETA_UNIT, ' '), a.BETA_DIRECTION)
+        ELSE a.DESCRIPTION END)                                  AS CI_QUALIFIER,
+       p.MANUFACTURER,
+       s.QUALIFIER,
+       s.SNP_COUNT,
+       s.IMPUTED,
+       s.STUDY_DESIGN_COMMENT,
+       s.PLATFORM,
+       s.CNV,
+       a.ID                                                      AS ASSOCIATION_ID,
+       s.ID                                                      AS STUDY_ID,
+       h.CATALOG_PUBLISH_DATE,
+       h.CATALOG_UNPUBLISH_DATE,
+       e.TRAIT,
+       e.URI
+     FROM STUDY s
+       JOIN PUBLICATION pub ON s.PUBLICATION_ID = pub.ID
+       JOIN AUTHOR auth on pub.FIRST_AUTHOR_ID = auth.ID
+       JOIN HOUSEKEEPING h ON h.ID = s.HOUSEKEEPING_ID
+       JOIN CURATION_STATUS cs ON h.CURATION_STATUS_ID = cs.ID
+       LEFT JOIN STUDY_DISEASE_TRAIT sdt ON sdt.STUDY_ID = s.ID
+       LEFT JOIN DISEASE_TRAIT dt ON dt.ID = sdt.DISEASE_TRAIT_ID
+       LEFT JOIN ASSOCIATION a ON a.STUDY_ID = s.ID
+       LEFT JOIN ASSOCIATION_LOCUS al ON al.ASSOCIATION_ID = a.ID
+       LEFT JOIN LOCUS_RISK_ALLELE lra ON lra.LOCUS_ID = al.LOCUS_ID
+       LEFT JOIN RISK_ALLELE ra ON ra.ID = lra.RISK_ALLELE_ID
+       LEFT JOIN RISK_ALLELE_SNP ras ON ras.RISK_ALLELE_ID = lra.RISK_ALLELE_ID
+       LEFT JOIN SINGLE_NUCLEOTIDE_POLYMORPHISM snp ON snp.ID = ras.SNP_ID
+       LEFT JOIN SNP_LOCATION ls ON ls.SNP_ID = snp.ID
+       LEFT JOIN LOCATION loc ON ls.LOCATION_ID = loc.id
+       LEFT JOIN REGION r ON r.ID = loc.REGION_ID
+       LEFT JOIN AUTHOR_REPORTED_GENE arg ON arg.LOCUS_ID = al.LOCUS_ID
+       LEFT JOIN GENE rg ON rg.ID = arg.REPORTED_GENE_ID
+       LEFT JOIN ASSOCIATION_EFO_TRAIT ae ON ae.ASSOCIATION_ID = a.ID
+       LEFT JOIN STUDY_PLATFORM sp ON sp.STUDY_ID = s.ID
+       LEFT JOIN PLATFORM p ON p.ID = sp.PLATFORM_ID
+       LEFT JOIN EFO_TRAIT e ON e.ID = ae.EFO_TRAIT_ID
+     ORDER BY pub.PUBLICATION_DATE DESC) V;

goci-interfaces/goci-curation/src/main/java/uk/ac/ebi/spot/goci/curation/service/FtpFileService.java

@@ -73,7 +73,7 @@ public void ftpFileUpload(File outputFile) throws IOException {
                     "Unable to connect to FTP. Max attempts exceeded.");
         }
 
-        /*
+
         InputStream inputStream = new FileInputStream(outputFile);
         String remoteFile = "gwas.txt";
 
@@ -87,7 +87,7 @@ public void ftpFileUpload(File outputFile) throws IOException {
             getLog().error("Failed to upload file " + remoteFile + " to FTP");
         }
 
-        */
+
         // Close FTP connection
         disconnect();
     }